[gmx-users] g_mindist periodic boundary condition

Dian Jiao oscarjiao at gmail.com
Thu Mar 4 01:30:03 CET 2010

Hi Gromacs users,

I was trying to compute minimum distance between groups in a cubic water box
with g_mindist using periodic boundary condition. In order to test this, I
added one more "atom" which is far away from any of the other atoms in the
pdb file. The mindist between that atom and all the waters were computed.
The output of g_mindist is 3.089281e+00. (the unit is nm, right?)

The manual shows that pbc is one of the option of g_mindist, but isn't the
default "yes"? I even tried with "-pbc" in the command, still did not work.
Can anyone tell me how to turn on PBC in g_mindist?


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